Commits for angie

v308_base to v309_preview (2014-11-03 to 2014-11-10) v309

• Adding .gitignore's for test output cruddies.
  • src/hg/autoSql/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/embossToPsl/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/estOrient/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/gbGetEntries/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/genePredHisto/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/genePredSingleCover/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/genePredToGtf/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/genePredToMafFrames/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/hgGetAnn/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/liftOver/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/mouseStuff/axtChain/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/mouseStuff/axtToMaf/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/mouseStuff/axtToPsl/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToAxt/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToPsl/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/mouseStuff/netToAxt/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/mrnaToGene/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/pslDiff/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/pslHisto/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/pslPartition/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/pslSelect/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/pslStats/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/pslSwap/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/pslToBed/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/spideyToPsl/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/overlapSelect/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/refSeqGet/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/xmlToSql/test/chado/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/xmlToSql/test/hotnews/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/xmlToSql/test/snp/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/utils/bedToBigBed/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/utils/faFilter/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/utils/faRandomize/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/utils/faToTwoBit/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/utils/pslLiftSubrangeBlat/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/utils/pslScore/tests/.gitignore - lines changed 2, context: html, text, full: html, text
• Moved dbSNP tracks out of hg38/hg38.txt and into hg38/variation.txt.
  • src/hg/makeDb/doc/hg38/hg38.txt - lines changed 589, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/variation.txt - lines changed 604, context: html, text, full: html, text
• Built snp142 tracks on hg19 & hg38.
  Checked for missing rs_fasta and there wasn't any this time! dbSNP provided
  a file of 1000 Genomes Phase3 indels that changed position and/or allele;
  the file had some issues and didn't come with rs_fasta changes so I decided
  to leave it as-is.
  
  hg19 still had incorrect weights for variants that uniquely mapped to a
  chrom and its alt(s); tweaked those to 1 when we didn't see MultipleAlignments.
  hg38 was OK though.
  
  refs #14189
  
  • src/hg/makeDb/doc/hg19.txt - lines changed 341, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/variation.txt - lines changed 290, context: html, text, full: html, text
  • src/hg/utils/automation/doDbSnp.pl - lines changed 28, context: html, text, full: html, text
• Registering track handlers for snp142 tracks.refs #14189
  
  • src/hg/hgTracks/simpleTracks.c - lines changed 4, context: html, text, full: html, text
• Adding trackDb entries for snp142.refs #14189
  
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 107, context: html, text, full: html, text
• Better display of allele count total for SNPs tracks -- before I wasextrapolating total2N from frequency but that isn't precise enough for
  very low frequencies.
  
  • src/hg/hgc/hgc.c - lines changed 6, context: html, text, full: html, text
• Loaded up DGV's update from mid-October; this is the first DGV release for hg38.Variant subtype keywords changed since last time.
  refs #14188
  
  • src/hg/makeDb/doc/hg18.txt - lines changed 38, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 40, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/variation.txt - lines changed 54, context: html, text, full: html, text
  • src/hg/utils/automation/translateDgvPlus.pl - lines changed 12, context: html, text, full: html, text
• Added release alpha / release beta,public stanzas for dgvPlus because dataVersion changed.refs #14188
  
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 17, context: html, text, full: html, text
• Added descriptions for snp142 tracks. refs #14189
  • src/hg/makeDb/trackDb/human/snp142.html - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/snp142.shared.html - lines changed 467, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/snp142Common.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/snp142Flagged.html - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/snp142Mult.html - lines changed 25, context: html, text, full: html, text